The gill chamber epibiosis of deep‐sea shrimp R imicaris exoculata : an in‐depth metagenomic investigation and discovery of Z etaproteobacteria

Abstract

Summary The gill chamber of deep‐sea hydrothermal vent shrimp R imicaris exoculata hosts a dense community of epibiotic bacteria dominated by filamentous E psilonproteobacteria and G ammaproteobacteria . Using metagenomics on shrimp from the R ainbow hydrothermal vent field, we showed that both epibiont groups have the potential to grow autotrophically and oxidize reduced sulfur compounds or hydrogen with oxygen or nitrate. For carbon fixation, the E psilonproteobacteria use the reductive tricarboxylic acid cycle, whereas the G ammaproteobacteria use the C alvin– B enson– B assham cycle. Only the epsilonproteobacterial epibionts had the genes necessary for producing ammonium. This ability likely minimizes direct competition between epibionts and also broadens the spectrum of environmental conditions that the shrimp may successfully inhabit. We identified genes likely to be involved in shrimp–epibiont interactions, as well as genes for nutritional and detoxification processes that might benefit the host. Shrimp epibionts at R ainbow are often coated with iron oxyhydroxides, whose origin is intensely debated. We identified 16 S rRNA sequences and functional genes affiliated with iron‐oxidizing Z etaproteobacteria , which indicates that biological iron oxidation might play a role in forming these deposits. Fluorescence in situ hybridizations confirmed the presence of active Z etaproteobacteria in the R . exoculata gill chamber, thus providing the first evidence for a Z etaproteobacteria– invertebrate association.

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